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Monobody-mediated alteration of enzyme specificity

Nature Chemical Biology volume 11, pages 762–764 (2015)Cite this article

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Abstract

Current methods for engineering enzymes modify enzymes themselves and require a detailed mechanistic understanding or a high-throughput assay. Here, we describe a new approach where catalytic properties are modulated with synthetic binding proteins, termed monobodies, directed to an unmodified enzyme. Using the example of a β-galactosidase from Bacillus circulans, we efficiently identified monobodies that restricted its substrates for its transgalactosylation reaction and selectively enhanced the production of small oligosaccharide prebiotics.

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Figure 1: Modulation of enzyme catalytic properties with synthetic binding proteins.
Figure 2: Monobodies modulate catalytic properties of BgaD-D.

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References

  1. Wilks, H.M. et al. Science 242, 1541–1544 (1988).

    Article  CAS  Google Scholar 

  2. Chen, K.Q. & Arnold, F.H. BioTechnology 9, 1073–1077 (1991).

    Article  CAS  Google Scholar 

  3. Bornscheuer, U.T. et al. Nature 485, 185–194 (2012).

    Article  CAS  Google Scholar 

  4. Davids, T., Schmidt, M., Bottcher, D. & Bornscheuer, U.T. Curr. Opin. Chem. Biol. 17, 215–220 (2013).

    Article  CAS  Google Scholar 

  5. Goldsmith, M. & Tawfik, D.S. Curr. Opin. Struct. Biol. 22, 406–412 (2012).

    Article  CAS  Google Scholar 

  6. Mak, W.S. & Siegel, J.B. Curr. Opin. Struct. Biol. 27, 87–94 (2014).

    Article  CAS  Google Scholar 

  7. Song, J. et al. Biosci. Biotechnol. Biochem. 75, 1194–1197 (2011).

    Article  CAS  Google Scholar 

  8. Barile, D. & Rastall, R.A. Curr. Opin. Biotechnol. 24, 214–219 (2013).

    Article  CAS  Google Scholar 

  9. Bultema, J.B., Kuipers, B.J. & Dijkhuizen, L. FEBS Open Bio 4, 1015–1020 (2014).

    Article  CAS  Google Scholar 

  10. Song, J. et al. Biosci. Biotechnol. Biochem. 75, 268–278 (2011).

    Article  CAS  Google Scholar 

  11. Ishikawa, K. et al. FEBS J. 282, 2540–2552 (2015).

    Article  CAS  Google Scholar 

  12. Strokopytov, B. et al. Biochemistry 34, 2234–2240 (1995).

    Article  CAS  Google Scholar 

  13. Vocadlo, D.J., Davies, G.J., Laine, R. & Withers, S.G. Nature 412, 835–838 (2001).

    Article  CAS  Google Scholar 

  14. Blake, C.C. et al. Proc. R. Soc. Lond. B Biol. Sci. 167, 378–388 (1967).

    Article  CAS  Google Scholar 

  15. Davies, G.J., Wilson, K.S. & Henrissat, B. Biochem. J. 321, 557–559 (1997).

    Article  CAS  Google Scholar 

  16. van der Veen, B.A. et al. J. Mol. Biol. 296, 1027–1038 (2000).

    Article  CAS  Google Scholar 

  17. Chen-Goodspeed, M., Sogorb, M.A., Wu, F. & Raushel, F.M. Biochemistry 40, 1332–1339 (2001).

    Article  CAS  Google Scholar 

  18. Schmitt, J., Brocca, S., Schmid, R.D. & Pleiss, J. Protein Eng. 15, 595–601 (2002).

    Article  CAS  Google Scholar 

  19. Koide, A., Bailey, C.W., Huang, X. & Koide, S. J. Mol. Biol. 284, 1141–1151 (1998).

    Article  CAS  Google Scholar 

  20. Koide, A., Wojcik, J., Gilbreth, R.N., Hoey, R.J. & Koide, S. J. Mol. Biol. 415, 393–405 (2012).

    Article  CAS  Google Scholar 

  21. Wojcik, J. et al. Nat. Struct. Mol. Biol. 17, 519–527 (2010).

    Article  CAS  Google Scholar 

  22. Gilbreth, R.N. et al. Proc. Natl. Acad. Sci. USA 108, 7751–7756 (2011).

    Article  CAS  Google Scholar 

  23. Sha, F. et al. Proc. Natl. Acad. Sci. USA 110, 14924–14929 (2013).

    Article  CAS  Google Scholar 

  24. Albayrak, N. & Yang, S.T. Biotechnol. Bioeng. 77, 8–19 (2002).

    Article  CAS  Google Scholar 

  25. Li, S., Yang, X., Yang, S., Zhu, M. & Wang, X. Comput Struct. Biotechnol. J. 2, e201209017 (2012).

    Article  Google Scholar 

  26. Koide, A., Gilbreth, R.N., Esaki, K., Tereshko, V. & Koide, S. Proc. Natl. Acad. Sci. USA 104, 6632–6637 (2007).

    Article  CAS  Google Scholar 

  27. Larkin, M.A. et al. Bioinformatics 23, 2947–2948 (2007).

    Article  CAS  Google Scholar 

  28. Goujon, M. et al. Nucleic Acids Res. 38, W695–W699 (2010).

    Article  CAS  Google Scholar 

  29. Koide, S., Koide, A. & Lipovsek, D. Methods Enzymol. 503, 135–156 (2012).

    Article  CAS  Google Scholar 

  30. Nishikori, S. et al. J. Mol. Biol. 424, 391–399 (2012).

    Article  CAS  Google Scholar 

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Acknowledgements

We acknowledge the use of the University of Chicago Genomics Core, which is supported by US National Institutes of Health grant P30CA014599 to the University of Chicago Comprehensive Cancer Center.

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Authors and Affiliations

  1. Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois, USA

    Shun-ichi Tanaka, Akiko Koide & Shohei Koide

  2. Frontier Research Department, Gifu R&D Center, Amano Enzyme, Inc., Gifu, Japan

    Shun-ichi Tanaka, Tetsuya Takahashi, Satoru Ishihara & Satoshi Koikeda

Authors
  1. Shun-ichi Tanaka
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  2. Tetsuya Takahashi
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  3. Akiko Koide
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  4. Satoru Ishihara
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  5. Satoshi Koikeda
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  6. Shohei Koide
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Contributions

S.T. and S. Koide designed the research. S.T. and A.K. generated and characterized the monobodies. S.T. and T.T. analyzed effects of the monobodies on enzyme reactions. T.T. and S.I. conducted mutagenesis analysis of BgaD. S. Koikeda and S. Koide supervised the research. S.T. and S. Koide wrote the manuscript and the other authors commented on it.

Corresponding author

Correspondence to Shohei Koide.

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Competing interests

S. Tanaka, T. Takahashi, S. Ishihara and S. Koikeda are employees of Amano Enzyme that manufactures the Biolacta enzyme. S. Tanaka, T. Takahashi and S. Koikeda are shareholders of Amano Enzyme. The University of Chicago has filed a patent application on technologies described in this paper.

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Supplementary Results, Supplementary Figures 1–8 and Supplementary Table 1. (PDF 2143 kb)

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Tanaka, Si., Takahashi, T., Koide, A. et al. Monobody-mediated alteration of enzyme specificity. Nat Chem Biol 11, 762–764 (2015). https://doi.org/10.1038/nchembio.1896

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